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Hett T, Zbik T, Mukherjee S, Matsuoka H, Bönigk W, Klose D, Rouillon C, Brenner N, Peuker S, Klement R, Steinhoff HJ, Grubmüller H, Seifert R, Schiemann O, Kaupp UB. Spatiotemporal Resolution of Conformational Changes in Biomolecules by Combining Pulsed Electron-Electron Double Resonance Spectroscopy with Microsecond Freeze-Hyperquenching. J Am Chem Soc 2021; 143:6981-6989. [PMID: 33905249 DOI: 10.1021/jacs.1c01081] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The function of proteins is linked to their conformations that can be resolved with several high-resolution methods. However, only a few methods can provide the temporal order of intermediates and conformational changes, with each having its limitations. Here, we combine pulsed electron-electron double resonance spectroscopy with a microsecond freeze-hyperquenching setup to achieve spatiotemporal resolution in the angstrom range and lower microsecond time scale. We show that the conformational change of the Cα-helix in the cyclic nucleotide-binding domain of the Mesorhizobium loti potassium channel occurs within about 150 μs and can be resolved with angstrom precision. Thus, this approach holds great promise for obtaining 4D landscapes of conformational changes in biomolecules.
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Affiliation(s)
- Tobias Hett
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Tobias Zbik
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Shatanik Mukherjee
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Hideto Matsuoka
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Wolfgang Bönigk
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Daniel Klose
- Fachbereich Physik, Universität Osnabrück, Barbarastraße 7, 49076 Osnabrück, Germany
| | - Christophe Rouillon
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Norbert Brenner
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Sebastian Peuker
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Reinhard Klement
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Reinhard Seifert
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - U Benjamin Kaupp
- Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.,Life & Medical Sciences Institute (LIMES), University of Bonn, Carl-Troll-Straße 31, 53115 Bonn, Germany
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Prabhakant A, Panigrahi A, Krishnan M. Allosteric Response of DNA Recognition Helices of Catabolite Activator Protein to cAMP and DNA Binding. J Chem Inf Model 2020; 60:6366-6376. [PMID: 33108170 DOI: 10.1021/acs.jcim.0c00617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The homodimeric catabolite activator protein (CAP) regulates the transcription of several bacterial genes based on the cellular concentration of cyclic adenosine monophosphate (cAMP). The binding of cAMP to CAP triggers allosteric communication between the cAMP binding domains (CBD) and DNA binding domains (DBD) of CAP, which entails repositioning of DNA recognition helices (F-helices) in the DBD to dock favorably to the target DNA. Despite considerable progress, much remains to be understood about the mechanistic details of DNA recognition by CAP and about the map of allosteric pathways involved in CAP-mediated gene transcription. The present study uses molecular dynamics and umbrella sampling simulations to investigate the mechanism of cAMP- and DNA-induced changes in the conformation and energetics of F-helices observed during the allosteric regulation of CAP by cAMP and the subsequent binding to the DNA promoter region. Using novel collective variables, the free energy profiles associated with the orientation and dynamics of F-helices in the unliganded, cAMP-bound, and cAMP-DNA-bound states of CAP are calculated and compared. The binding-induced alterations in the resultant free energy profiles reveal important flexibility constraints imposed on DBD upon cAMP and DNA binding. A comprehensive analysis of residue-wise interaction maps reveals potential allosteric pathways between CBD and DBD that facilitate the allosteric transduction of regulatory signals in CAP. The revelation that the predicted allosteric pathways crisscross the intersubunit interface offers important clues on the microscopic origin of the intersubunit cooperativity and dimer stability of CAP.
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Affiliation(s)
- Akshay Prabhakant
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology, Gachibowli, Hyderabad, Telangana 500032, India
| | - Abhinandan Panigrahi
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology, Gachibowli, Hyderabad, Telangana 500032, India
| | - Marimuthu Krishnan
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology, Gachibowli, Hyderabad, Telangana 500032, India
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Rico F, Russek A, González L, Grubmüller H, Scheuring S. Heterogeneous and rate-dependent streptavidin-biotin unbinding revealed by high-speed force spectroscopy and atomistic simulations. Proc Natl Acad Sci U S A 2019; 116:6594-6601. [PMID: 30890636 PMCID: PMC6452689 DOI: 10.1073/pnas.1816909116] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Receptor-ligand interactions are essential for biological function and their binding strength is commonly explained in terms of static lock-and-key models based on molecular complementarity. However, detailed information on the full unbinding pathway is often lacking due, in part, to the static nature of atomic structures and ensemble averaging inherent to bulk biophysics approaches. Here we combine molecular dynamics and high-speed force spectroscopy on the streptavidin-biotin complex to determine the binding strength and unbinding pathways over the widest dynamic range. Experiment and simulation show excellent agreement at overlapping velocities and provided evidence of the unbinding mechanisms. During unbinding, biotin crosses multiple energy barriers and visits various intermediate states far from the binding pocket, while streptavidin undergoes transient induced fits, all varying with loading rate. This multistate process slows down the transition to the unbound state and favors rebinding, thus explaining the long lifetime of the complex. We provide an atomistic, dynamic picture of the unbinding process, replacing a simple two-state picture with one that involves many routes to the lock and rate-dependent induced-fit motions for intermediates, which might be relevant for other receptor-ligand bonds.
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Affiliation(s)
- Felix Rico
- Laboratoire Adhésion et Inflammation (LAI), Aix-Marseille Université, CNRS, INSERM, 13009 Marseille, France;
| | - Andreas Russek
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Laura González
- Department of Electronics, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;
| | - Simon Scheuring
- Department of Anesthesiology, Weill Cornell Medical College, New York, NY 10065;
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065
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Thermodynamics of camphor migration in cytochrome P450cam by atomistic simulations. Sci Rep 2017; 7:7736. [PMID: 28798338 PMCID: PMC5552751 DOI: 10.1038/s41598-017-07993-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/05/2017] [Indexed: 01/12/2023] Open
Abstract
Understanding the mechanisms of ligand binding to enzymes is of paramount importance for the design of new drugs. Here, we report on the use of a novel biased molecular dynamics (MD) methodology to study the mechanism of camphor binding to cytochrome P450cam. Microsecond-long MD simulations allowed us to observe reaction coordinates characterizing ligand diffusion from the active site of cytochrome P450cam to solvent via three egress routes. These atomistic simulations were used to estimate thermodynamic quantities along the reaction coordinates and indicate diverse binding configurations. The results suggest that the diffusion of camphor along the pathway near the substrate recognition site (SRS) is thermodynamically preferred. In addition, we show that the diffusion near the SRS is triggered by a transition from a heterogeneous collection of closed ligand-bound conformers to the basin comprising the open conformations of cytochrome P450cam. The conformational change accompanying this switch is characterized by the retraction of the F and G helices and the disorder of the B' helix. These results are corroborated by experimental studies and provide detailed insight into ligand binding and conformational behavior of the cytochrome family. The presented methodology is general and can be applied to other ligand-protein systems.
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